Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	Exported	194,926:1	+T	23.3%	intergenic (+122/+78)	nlpE → / ← yaeF	lipoprotein involved with copper homeostasis and adhesion/predicted lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	Exported	194,926	1	.	T	23.3%	90.2 / 30.0	30	intergenic (+122/+78)	nlpE/yaeF	lipoprotein involved with copper homeostasis and adhesion/predicted lipoprotein
Reads supporting (aligned to +/- strand):  ref base . (7/16);  new base T (4/3);  total (11/19)
Fisher's exact test for biased strand distribution p-value = 3.72e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.80e-01

CACGTTTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACAACCCCCCTCATACCTTAAGGCGGA  >  Exported/194870‑194987                                                          |                                                              cACGTTTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATGGTGCTCAAC‑GCCTGATGCGACg                                                  <  1:1848405/70‑1 (MQ=255) cACGTTTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATGGTGCTCAAC‑GCCTGATGCGACg                                                  <  1:4878981/70‑1 (MQ=255)      tttttGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATGGTGCTCAAC‑GCCTGATGCGACGCTGgcg                                            >  1:823979/1‑71 (MQ=255)      tttttGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATGGTGCTCAAC‑GCCTGATGCGACGCTGgc                                             >  1:4768027/1‑70 (MQ=255)        tccgTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACAGTGC‑CAACTGCCTGATGCGACGCTCgcgc                                           >  1:3064589/4‑70 (MQ=11)         ccgTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACAGTGC‑CAACTGCCTGATGCGACGCTTGCGCGt                                         >  1:4934577/3‑71 (MQ=11)          cgTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAACAGTGC‑CAACTGCCTGATGCGACGCTTGCGCGTc                                        >  1:3941813/2‑71 (MQ=11)            tAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCtt                                      <  1:1143037/71‑1 (MQ=255)            tAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCtt                                      <  1:5137867/71‑1 (MQ=255)              ggCCGGATAAGGCGTTTACGCCGCATCCGGCAACAGTGC‑CAACTGCCTGATGCGACGCTTGCGCGTCTTAt                                    <  1:1916953/71‑1 (MQ=11)               gCCGGATAAGGCGTTTACGCCGCATCCGGCAATGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTAt                                    <  1:5507982/70‑1 (MQ=255)               gCCGGATAAGGCGTTTACGCCGCATCCGGCAACAGTGC‑CAACTGCCTGATGCGACGCTTGCGCGTCTTATc                                   <  1:4794087/71‑1 (MQ=11)                ccGTATAAGGCGTTTACGCCGCATCCGGCAACAGTGC‑CAACTGCCTGATGCGACGCTTGCGCGTCTTAt                                    <  1:1212443/69‑1 (MQ=11)                   gATAAGGCGTTTACGCCGCATCCGGCAATGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTATCATGc                               >  1:883738/1‑71 (MQ=255)                         gCGTTTACGCCGCATCCGGCAATGGTGCTCAAC‑GCCTGATGCGACGCTg                                               <  1:957765/49‑1 (MQ=255)                         gCGTTTACGCCGCATCCGGCAACAGTGC‑CAACTGCCTGATGCGACGCTTGCGCGTCTTATCAGGCCTACa                          >  1:1408254/1‑70 (MQ=1)                           gTTTACGCCGCATCCGGCAATGGTGCCGACT‑GCCTGATGCGACGCTTGCGCGTCTTATCAGGCCTACaaat                       <  1:5002092/71‑3 (MQ=11)                             ttACGCCGCATCCGGCAATGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTATCa                                  >  1:5319103/1‑58 (MQ=255)                                      aTCCGGCAATGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACAACCCCCCTCATAcc            >  1:4895975/1‑71 (MQ=255)                                       tCCGGCAATGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACAACCCCCCTCATACCt           <  1:5325089/71‑1 (MQ=255)                                          ggCAATGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACAACCCCCCTCATACCTTaa        <  1:3645414/71‑1 (MQ=255)                                          ggCAATGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACAACCCCCCTCATACCTTaa        <  1:3638862/71‑1 (MQ=255)                                              aTGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACAACCCCCCTCAt               <  1:4839344/60‑1 (MQ=255)                                              aTGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACAACCCCCCTCAt               <  1:4844560/60‑1 (MQ=255)                                              aTGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACAACCCCCCTCAt               <  1:103898/60‑1 (MQ=255)                                              aTGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACAACCCCCCTCATACCTTAAGGCg    <  1:4997723/71‑1 (MQ=255)                                                 gTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACAACCCCCCTCATACCTTAAGGCGGa  <  1:2437194/70‑1 (MQ=255)                                                 gTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACAACCCCCCTCATACCTTAAGGCGGa  >  1:1363025/1‑70 (MQ=255)                                                       aaC‑GCCTGATGCGACGCTGGCGCGTCTTATCATGCCTa                            >  1:5123926/1‑38 (MQ=40)                                                        aC‑GCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACAACCCCCCTCATACCTTAAGGCgg   <  1:451821/62‑1 (MQ=255)                                                          |                                                              CACGTTTTTTGTAGGCCGGATAAGGCGTTTACGCCGCATCCGGCAATGGTGCTCAAC‑GCCTGATGCGACGCTGGCGCGTCTTATCATGCCTACAACCCCCCTCATACCTTAAGGCGGA  >  Exported/194870‑194987

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑